2. Logan might be an XXY man. Probably not, because he doesn't fit the body type for an XXY man, though that could be the result of his mutation. If he IS an XXY man, though, then if the clone somehow lost the Y chromosome, she would be a girl and would be an imperfect clone.

3. Maybe Laura is a trans girl somehow?

4. Maybe Logan is a normal XY man and in the cloning process Laura lost the Y chromosome? Probably not, because her body doesn't match Turner Syndrome. Unless maybe her mutant gene cancelled that out?

5. Another possibility is Logan is an XXXY male, but since the effects are similar to XXY only more so, this is also unlikely.

6. Maybe Logan has some other kind of intersex condition, one that's not genetic but something in the womb, to make him genetically XX but somehow male, like some gene got copied wrong and made him grow testicles?

If it's not true:

1. Perhaps Laura isn't a clone at all, just mostly a clone; maybe they removed the Y chromosome for some reason and put in a second X chromosome. I don't see why they'd do that unless they just wanted to see what would happen, though, because there's no way to know how a new X chromosome, even if you just copied the original X chromosome and stuck it in there, would change the resulting organism. But again, maybe they just wanted to see what would happen.

2. Or Laura isn't a clone at all, in another way: maybe they just took someone else's DNA and attached Logan's mutant gene to it, making her genetically engineered, and still in a sense her father, just not a clone.